Ah, I misread the OP.... I thought you were marking it "read" and wanting it to show up in your list.
Yes, if you are marking it "unread", it absolutely should stay on the list, and remember where you were at the time. Hopefully what happened was a one-off. With a database this big, I guess a glitch every so often might happen, although it's certainly annoying and I wish there were never glitches.